Moved to new package

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala

@@ -3,7 +3,7 @@
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
  */
-package nl.lumc.sasc.biopet.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.gatk.{ GenotypeGVCFs, SelectVariants }
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{ SelectVariants, GenotypeGVCFs }
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -10,9 +10,9 @@ import nl.lumc.sasc.biopet.core.PipelineCommand
 import nl.lumc.sasc.biopet.core.config.Configurable
 import htsjdk.samtools.SamReaderFactory
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CombineVariants, CombineGVCFs }
 import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import scala.collection.JavaConversions._
-import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, CombineGVCFs }
 import nl.lumc.sasc.biopet.extensions.picard.AddOrReplaceReadGroups
 import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala

@@ -8,9 +8,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 import nl.lumc.sasc.biopet.core.BiopetQScript
 import nl.lumc.sasc.biopet.core.PipelineCommand
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.gatk.ApplyRecalibration
-import nl.lumc.sasc.biopet.extensions.gatk.VariantAnnotator
-import nl.lumc.sasc.biopet.extensions.gatk.VariantRecalibrator
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{ ApplyRecalibration, VariantAnnotator, VariantRecalibrator }
 import org.broadinstitute.gatk.queue.QScript
 
 class GatkVariantRecalibration(val root: Configurable) extends QScript with BiopetQScript {

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

@@ -8,9 +8,9 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import java.io.File
 import nl.lumc.sasc.biopet.extensions.Ln
+import nl.lumc.sasc.biopet.extensions.gatk.broad._
 import nl.lumc.sasc.biopet.tools.{ VcfStats, MpileupToVcf, VcfFilter, MergeAlleles }
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.gatk.{ AnalyzeCovariates, BaseRecalibrator, GenotypeGVCFs, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, SelectVariants, CombineVariants, UnifiedGenotyper }
 import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript